Angela Mayes thought she was ahead of the game. Months before moving from North Carolina, she preregistered her son online for the Boston public schools, choosing the school closest to the South End apartment where they’d be living.

But early in September, she received a swift and unsettling education in the school district’s Byzantine school assignment process. He wasn’t yet registered - he couldn’t be until she brought in proof of her new address - and he was never guaranteed a spot in the neighborhood school, anyway.

Two days before school started, she found her son on a wait list to get into a public elementary school, a completely foreign concept she struggled to accept. And no one could assure her where he’d be assigned - or when.

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“Oh, my God,’’ Mayes said. “I’m freaking out.’’

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School opened with almost 10,000 students - nearly 18 percent of the student body - still on waiting lists, trying to get into different schools than they were assigned. Some, like Mayes’s son, were held up because they came late to the process. Others applied on time but were disappointed by their assignments and hoping for better placements.

Most would never get called. Those who did might wait days or weeks for an opening. Some might not be notified of vacancies until November, forcing families to make agonizing decisions about pulling children out of classrooms they have grown used to.

Boston’s school lottery is a balancing act. Designed to give every family a chance at getting into a high-achieving school, the lottery lets parents request seats in schools outside their neighborhoods. The intent is to spread opportunity in a city with uneven schools and keep options open for parents, but the unintended consequence, too often, is disruption. Since school started in September, about 750 students moved off waiting lists and into different schools, leaving altered class lists and new vacancies to be filled behind them.

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Last-minute changes are inevitable in a city with a highly mobile population, where hundreds of students move during the summer, but Boston’s assignment system adds - and indeed fosters - additional layers of delay and uncertainty.

Families who were asked to choose a school last winter or spring were never forced to commit to one. Students could show up - or not - in September. If they didn’t, the district left their seats open for eight school days before releasing the spots to wait-listed students, tying up thousands of seats for the first two weeks of school. The number of no-shows, eight days into this school year, was 2,810.

Yoon S. Byun/Globe Staff

“How are you supposed to choose a school if you don’t even know about the schools or where they’re located?” - Mattan parent Mariah Williams, on trying to register her son for kindergarten

With about 18 schools that closed or merged last summer, enrollments are tight and almost every classroom in the city has a waiting list. Some lists stretch so long that families have no reasonable hope of transferring in. (The Murphy K-8 School had 200 children on the waiting list for kindergarten in late September.)

The long waiting lists add more variables at a time when the district is already trying to absorb students who registered at the last minute. In the final weeks before school started, hundreds of parents registered their children for the first time, expecting them to start school in September at whatever school was closest. This year, the number was even steeper than usual: 1,705 students registered after mid-August, up from 1,500 last year, said Denise Snyder, the senior director of enrollment and welcome services. The latecomers had to settle for the few schools with open seats or get in line behind students who were already on waiting lists.

Some couldn’t immediately get assigned to any school at all. The day before school started, 183 students did not have a seat anywhere. Matthew Wilder, a school district spokesman, said those students had come in late and their paperwork was being processed, which typically takes a day or two.

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Mayes’s son found himself worse off: He missed the first five days of school because the district had no place to put him. His mother taught him lessons downloaded from the Web in between her work assignments. When he was finally assigned to a school in Allston, he missed more days because Mayes, anticipating a longer wait, had booked a trip back to North Carolina.

‘We looked at each other and said, we can’t do this anymore.’

Mayes was part of the second wave of parents flooding the system, months after the first wave had tried to stake its claim. Ambitious parents had obsessed over the school lottery last winter, agonizing over their choices and trading tips online for how to get into the schools with the highest test scores and the safest reputations. By late summer, those families had nailed down seats - and spots on waiting lists - and a whole new crop of parents was emerging.

The late arrivals flooded Family Resource Centers seeking schools less for their academic reputation than their convenience - close to home, with after-school programs or bus access that could accommodate their work schedules. Some were vying for placement in schools that are hardly academic standouts. Mayes requested Blackstone Elementary School because of its proximity; it is also among the lowest-performing elementary schools in the state and a focus of the city’s school improvement efforts.

Yoon S. Byun/ Globe Staff

“We looked at each other and said, we can’t do this anymore.” - Jen Bowen-Flynn, whose daughter Sawyer (pictured with her father, Doug) was on a waiting list before her parents decided to home-school her in their North End home.

Some parents who came late were flummoxed. Mariah Williams of Mattapan sat in the East Zone Family Resource Center, trying to register her son for kindergarten on the day it started.

“I only know one school on here,’’ she said, staring at a long list of elementary schools. “How are you supposed to choose a school if you don’t even know about the schools or where they’re located?’’

Even well-prepared parents found themselves mired in uncertainty.

Olayemi Phillips of Mattapan had visited several schools last winter, seeking the one that would be the right fit for her daughter, before ranking nine choices. The assignment she got was a disappointment: Chittick Elementary School wasn’t in her top six. All summer long, they stayed on waiting lists, hoping for news of an opening at one of their preferred schools.

But when her daughter, a precocious early reader named Nia, started prekindergarten at Chittick, she made a new best friend and fell in love with her principal. She is, her mother said, the last to leave the playground every day. Phillips’s tepid initial reaction to the school - “We don’t hate it’’ - gradually deepened into pride. Recently, she bought Nia a Chittick Elementary sweatshirt. She’s staying.

“I don’t see any reason whatsoever to [transfer] her,’’ Phillips said, three weeks into the school year. “She could not be happier. Any reservations or fears I had, they’re pretty much gone now.’’

Though she plans to take Nia’s name off other schools’ waiting lists, she hasn’t done so yet.

Families can stay on three different lists - up from two a few years ago - until January, hedging their bets.

The wide latitude given to families to stay on waiting lists and equivocate all summer on whether they will attend their designated school is frustrating to many.

“Anywhere else on earth, you have to let someone know that you’re coming to something. Why should school be different?’’ former city councilor John Tobin said eight years ago, when he held hearings on the issue and spurred the district to start requesting RSVPs.

But the RSVPs are only requested, not required. School officials say that many families’ circumstances change over the summer and acknowledge that, as a public school, they’re obligated to take in students, however late they respond.

“People have options and they’re going to keep their options open for as long as they can, and you can’t blame them for that,’’ said Maureen Lumley, the school ombudswoman who runs the parent hotline. “That’s just the way the game is played.’’

David L Ryan/Globe Staff

Families waited at a school district Family Resource Center at the start of the school year, trying to get a school assignment.

Waiting lists for public elementary schools often come as a shock to parents unfamiliar with Boston’s process. “What are they waiting for?’’ asked Mayes. “Somebody to die? Somebody to get kicked out of school? How is that going to work?’’

In late September, hotline worker Rakim Pinckney reached one mother whose child was No. 1 on Everett Elementary School’s kindergarten wait list; she eagerly claimed the spot offered. Attempting to reach another parent about an open seat, Pinckney tried all three numbers on the registration form: One was disconnected, one was a wrong number, and the third connected to a fax machine. With no way to leave a message, he moved down the list.

The vagaries of the waiting list have antagonized parents for years, leaving their plans in the air all summer.

Last January, when she was signing up her son for kindergarten, Mary Boyle of West Roxbury aimed for the Kilmer K-8 School in her neighborhood. At the same time, she asked to transfer her daughter there; if her son got in Kilmer, her preferred school, she didn’t want to be taking her daughter to a different elementary school with a different start time.

But Sarah Boyle sat at the top of Kilmer’s second-grade waiting list all summer. Her mother, who kept anxiously calling, was told not to expect news until the end of August.

“I have to call you the last week of August?’’ Boyle recounted, with incredulity. “Do you know school starts September 8? Where is my daughter going to school? How is it you can’t tell me?’’

Boyle didn’t get the call until two days after school started. Though she was thrilled to make the switch, she said it happened in a way that was unnecessarily disruptive.

“The two days is enough to fall in love with a teacher and see her friends,’’ Boyle said. “It could have been a lot smoother had we known before school started.’’

The Boyles’ gain may have been another family’s loss, however. Students with siblings in a school get preference over others - regardless of when they apply - frustrating families who see their waiting list numbers stall or even slip backwards as September approaches.

In the North End, where they live across the street from the Eliot K-8 School, Jen and Doug Bowen-Flynn tracked their daughter’s waiting list position at the school all summer. It never changed.

“We looked at each other and said, we can’t do this anymore,’’ Jen Bowen-Flynn said. “There’s a feeling of helplessness, putting your child’s educational welfare and your life on hold.’’

They finally gave up and decided to home-school the 4-year-old.

Officials acknowledge the late changes are disruptive. They suspend waiting list calls in October and early November to prevent transfers late in the first grading period.

But more importantly, they say, the waiting lists help compensate for the inequities of the lottery system. Not every family gets seats at the schools they want, but every family can take a gamble - again - on those seats opening up later on.

“The value of the wait list, in my view, is as an equalizer,’’ Snyder said.

Why does a school district that starts the assignment process so early not finish it before school starts? Administrators say they can’t start assignments until late in the summer because they have to wait for 3,000 students to finish summer school in August to find out who will actually be promoted and who will have to repeat a grade. The school district’s hotline, which fielded 15,000 calls in five weeks, only has a temporary staff of a dozen and only opened in late August.

“When folks get back from their vacations and hotline staff starts making the phone calls, parents are home, they’ve made decisions, it works,’’ said Jerry Burrell, director of enrollment and planning and support. “Any earlier, it just doesn’t work.’’

The district’s eight-day lag in filling seats ensures additional delays for most of the students who will move off waiting lists and into vacant spots.

Superintendent Carol Johnson said she assumes the eight-day time frame was meant to give parents who can’t be reached by phone adequate time to respond to a letter to explain their plans. Johnson noted that many of the district’s students are poor and have parents who are not native English speakers and are difficult to reach. Students may be intermittently homeless. Children are in foster care. Custody arrangements change.

“I think we have to probably be more sensitive to the transitions of families than a suburban district might have, because our kids tend to be more mobile and their families tend to struggle financially,’’ said Johnson.

But the systemic delay infuriates parents of wait-listed students whose own transitions are delayed for eight days. The volume of students still missing after that period has ended is staggering: nearly 5 percent of the student body.

“The thing that amazes me is that the system has become so apathetic to it, ’’ said Boyle. “It shouldn’t be okay that it happens all the time.’’

Johnson, the superintendent, said the district will study whether the eight-day period is appropriate, but she was surprised to hear parents like Mayes were being told they might have to wait up to two weeks for their children to start school.

“That’s not an acceptable response from us, under any stretch of the imagination,’’ Johnson said. “I don’t think a child should be sitting out that long. They should be placed immediately.’’

At the Allston school where Adrian was assigned, Jackson-Mann K-8 School, principal Andy Tuite welcomed the boy with a free backpack and a generous smile. The boy’s teacher warmly introduced him to each of his new classmates.

Mayes liked the school. But she wasn’t about to let her 6-year-old wait on the streets of an unfamiliar city each day to take a long bus ride across town.

Driving him has meant trimming her hours as a paramedical examiner and considering a $500-a-month after-school program.

The difficulty of signing her son up for school has soured her on Boston. She’s already requesting a work transfer back to North Carolina.

There’s only one thing that could change her mind: A call about an open seat at Blackstone Elementary School.